75 if (
_database_.nbRows() == std::size_t(0))
return;
83 const auto cols =
_database_.columnsFromVariableName(var_name);
87 "Variable " << var_name <<
" could not be found in the database")
97 "Variable of Id " <<
id <<
" could not be found in the database")
258 "setFCIMaxPathLength() is only valid when using the FCI algorithm")
266 "setFCIExhaustiveSepSet() is only valid when using the FCI algorithm")
274 "fciExhaustiveSepSet() is only valid when using the FCI algorithm")
315 "setPCMaxCondSetSize() is only valid when using the PC algorithm")
324 "setPCUnshieldedColliderSorted() is only valid when using the PC algorithm")
398 if ((noise < 0.0) || (noise > 1.0))
421 if ((noise < 0.0) || (noise > 1.0))
438 else GUM_ERROR(
NotFound,
"EM is currently forbidden. Please enable it with useEM()")
450 else return "EM is currently forbidden. Please enable it with useEM()";
615 for (
const auto& slice: slices) {
616 for (
const auto& name: slice) {
634 for (
const auto& name: order) {
699 "IBNLearner getPriorType does "
700 "not support yet this prior")
723 INLINE
const std::vector< std::pair< std::size_t, std::size_t > >&
780 std::string_view message) {
786 algoK2_.approximationScheme().setEpsilon(eps);
798 algoK2_.approximationScheme().disableEpsilon();
805 algoK2_.approximationScheme().enableEpsilon();
817 algoK2_.approximationScheme().setMinEpsilonRate(rate);
820 dag2BN_.setMinEpsilonRate(rate);
829 algoK2_.approximationScheme().disableMinEpsilonRate();
832 dag2BN_.disableMinEpsilonRate();
836 algoK2_.approximationScheme().enableMinEpsilonRate();
839 dag2BN_.enableMinEpsilonRate();
848 algoK2_.approximationScheme().setMaxIter(max);
860 algoK2_.approximationScheme().disableMaxIter();
867 algoK2_.approximationScheme().enableMaxIter();
879 algoK2_.approximationScheme().setMaxTime(timeout);
896 algoK2_.approximationScheme().disableMaxTime();
903 algoK2_.approximationScheme().enableMaxTime();
915 algoK2_.approximationScheme().setPeriodSize(p);
927 algoK2_.approximationScheme().setVerbosity(v);
975 return dag2BN_.isEnabledMinEpsilonRate();
1010 return dag2BN_.stateApproximationScheme();
A class for generic framework of learning algorithms that can easily be used.
The base class for all directed edges.
const EdgeSet & edges() const
returns the set of edges stored within the EdgeGraphPart
The base class for all undirected edges.
Exception : fatal (unknown ?) error.
value_type & insert(const Key &key, const Val &val)
Adds a new element (actually a copy of this element) into the hash table.
Signaler< Size, double, double > onProgress
Progression, error and time.
ApproximationSchemeSTATE
The different state of an approximation scheme.
Signaler< std::string_view > onStop
Criteria messageApproximationScheme.
Error: A name of variable is not found in the database.
Exception : the element we looked for cannot be found.
Exception : operation not allowed.
Exception : out of bound.
void insert(const Key &k)
void setNumberOfThreads(Size nb) override
sets the number max of threads to be used by the class containing this ThreadNumberManager
Base class for undirected graphs.
the class used to read a row in the database and to transform it into a set of DBRow instances that c...
The class representing a tabular database as used by learning tasks.
A class for parameterizing EM's parameter learning approximations.
const std::vector< std::string > & missingSymbols() const
returns the set of missing symbols taken into account
const DatabaseTable & databaseTable() const
returns the internal database table
std::size_t size() const
returns the number of records in the database
std::vector< std::size_t > _domain_sizes_
the domain sizes of the variables (useful to speed-up computations)
DatabaseTable _database_
the database itself
const std::string & nameFromId(NodeId id) const
returns the variable name corresponding to a given node id
double weight(const std::size_t i) const
returns the weight of the ith record
Bijection< NodeId, std::size_t > _nodeId2cols_
a bijection assigning to each variable name its NodeId
const std::vector< std::string > & names() const
returns the names of the variables in the database
void setWeight(const std::size_t i, const double weight)
sets the weight of the ith record
const Bijection< NodeId, std::size_t > & nodeId2Columns() const
returns the mapping between node ids and their columns in the database
DBRowGeneratorParser & parser()
returns the parser for the database
DBRowGeneratorParser * _parser_
the parser used for reading the database
NodeId idFromName(std::string_view var_name) const
returns the node id corresponding to a variable name
void setDatabaseWeight(const double new_weight)
assign a weight to all the rows of the database so that the sum of their weights is equal to new_weig...
std::size_t nbRows() const
returns the number of records in the database
const std::vector< std::size_t > & domainSizes() const
returns the domain sizes of the variables
double weight() const
returns the weight of the whole database
void usePC()
indicate that we wish to use PC (Chi2 test by default)
StructuralConstraintPossibleEdges constraintPossibleEdges_
the constraint on possible Edges
StructuralConstraintNoParentNodes constraintNoParentNodes_
the constraint on no parent nodes
Size periodSize() const override
how many samples between 2 stopping isEnableds
void eraseNoChildrenNode(NodeId node)
double recordWeight(const std::size_t i) const
returns the weight of the ith record
BNLearnerPriorType priorType_
the a priorselected for the score and parameters
bool EMisEnabledMaxTime() const
void EMenableEpsilon()
Enable the log-likelihood min diff stopping criterion in EM.
bool EMisEnabledEpsilon() const
return true if EM's stopping criterion is the log-likelihood min diff
void EMsetPeriodSize(Size p)
how many samples between 2 stoppings isEnabled
const std::vector< std::size_t > & domainSizes() const
returns the domain sizes of the variables in the database
Size nbrIterations() const override
void setMinEpsilonRate(double rate) override
Given that we approximate f(t), stopping criterion on d/dt(|f(t+1)-f(t)|) If the criterion was disabl...
void useGreedyHillClimbing()
indicate that we wish to use a greedy hill climbing algorithm
void useScoreBDeu()
indicate that we wish to use a BDeu score
void addNoParentNode(NodeId node)
Size EMnbrIterations() const
returns the number of iterations performed by the last EM execution
void enableMaxTime() override
stopping criterion on timeout If the criterion was disabled it will be enabled
void setSliceOrder(const NodeProperty< NodeId > &slice_order)
sets a partial order on the nodes
bool isUsingEM() const
indicates whether we use EM for parameter learning
bool isScoreBased() const
indicate if the selected algorithm is score-based
void setForbiddenArcs(const ArcSet &set)
removes a total
std::string priorDbname_
the filename for the Dirichlet a priori, if any
double priorWeight_
the weight of the prior
void enableEpsilon() override
Enable stopping criterion on epsilon.
double maxTime() const override
returns the timeout (in seconds)
double noiseEM_
the noise factor (in (0,1)) used by EM for perturbing the CPT during init
std::vector< std::pair< std::size_t, std::size_t > > ranges_
the set of rows' ranges within the database in which learning is done
void setDatabaseWeight(const double new_weight)
assign a weight to all the rows of the learning database so that the sum of their weights is equal to...
std::vector< Arc > latentVariables() const
get the list of arcs hiding latent variables
void useFCIChi2Test()
indicate that we wish to use Chi2 independence test for FCI
void clearDatabaseRanges()
reset the ranges to the one range corresponding to the whole database
std::string checkScorePriorCompatibility() const
checks whether the current score and prior are compatible
void useBDeuPrior(double weight=1.0)
use the BDeu prior
void setMandatoryArcs(const ArcSet &set)
assign a set of mandatory arcs
bool greedyThickThinningReversals() const
returns whether arc reversals are allowed in the thin phase of greedy thick-thinning
@ EXTENDED_GREEDY_HILL_CLIMBING
@ LOCAL_SEARCH_WITH_TABU_LIST
ApproximationSchemeSTATE EMState() const
returns the state of the last EM algorithm executed
void distributeStop(const ApproximationScheme *approximationScheme, std::string_view message)
distribute signals
bool allowArcTriangleDeletions_
whether we allow or not arc deletions during learning
void EMdisableMinEpsilonRate()
Disable the log-likelihood evolution rate stopping criterion.
void useExtendedGreedyHillClimbing()
indicate that we wish to use the extended greedy hill climbing algorithm
double EMMaxTime() const
@brief returns EM's timeout (in milliseconds)
void setFCIMaxPathLength(Size max_len)
set maximum discriminating-path length for FCI R4 (default Size(-1) = unlimited)
ApproximationSchemeSTATE EMStateApproximationScheme() const
get the current state of EM
const std::string & nameFromId(NodeId id) const
returns the variable name corresponding to a given node id
double databaseWeight() const
returns the weight of the whole database
const std::vector< double > & history() const override
void setMaxIter(Size max) override
stopping criterion on number of iterationsIf the criterion was disabled it will be enabled
K2 algoK2_
the K2 algorithm
IndepTestType indepTestTypeFCI_
independence test type for FCI (reuses IndepTestType defined above)
void addMandatoryArc(const Arc &arc)
AlgoType selectedAlgo_
the selected learning algorithm
const std::vector< std::pair< std::size_t, std::size_t > > & databaseRanges() const
returns the current database rows' ranges used for learning
void EMenableMaxIter()
Enable stopping criterion on max iterations.
void useFCI()
indicate that we wish to use FCI (Chi2 test by default)
void enableMinEpsilonRate() override
Enable stopping criterion on epsilon rate.
bool allowArcAdditions_
whether we allow or not arc additions during learning
void useFCIG2Test()
indicate that we wish to use G2 independence test for FCI
void setEpsilon(double eps) override
Given that we approximate f(t), stopping criterion on |f(t+1)-f(t)| If the criterion was disabled it ...
void setMaxIndegree(Size max_indegree)
sets the max indegree
void EMdisableEpsilon()
Disable the min log-likelihood diff stopping criterion for EM.
void addPossibleEdge(const Edge &edge)
bool isEnabledMaxIter() const override
void EMsetMaxIter(Size max)
add a max iteration stopping criterion
void useChi2Test()
indicate that we wish to use Chi2 independence test for PC
void setInitialDAG(const DAG &)
sets an initial DAG structure
void useK2(const Sequence< NodeId > &order)
indicate that we wish to use K2
Database scoreDatabase_
the database to be used by the scores and parameter estimators
void allowArcDeletions(bool allow=true)
allow (true)/forbid (false) to delete arcs during learning.
void setMaxTime(double timeout) override
stopping criterion on timeout If the criterion was disabled it will be enabled
double epsilon() const override
Get the value of epsilon.
double EMEpsilon() const
Get the value of EM's min diff epsilon.
bool useEM_
a Boolean indicating whether we should use EM for parameter learning or not
DAG2BNLearner dag2BN_
the parametric EM
void EMsetMinEpsilonRate(double rate)
sets the stopping criterion of EM as being the minimal log-likelihood's evolution rate
bool isEnabledMaxTime() const override
double EMMinEpsilonRate() const
Get the value of the minimal log-likelihood evolution rate of EM.
void distributeProgress(const ApproximationScheme *approximationScheme, Size pourcent, double error, double time)
{@ /// distribute signals
void setGreedyThickThinningReversals(bool allow)
enable or disable arc reversals in the thin phase of greedy thick-thinning
void setPeriodSize(Size p) override
how many samples between 2 stopping isEnableds
Size EMMaxIter() const
return the max number of iterations criterion
void disableMinEpsilonRate() override
Disable stopping criterion on epsilon rate.
void EMdisableMaxIter()
Disable stopping criterion on max iterations.
BNLearnerPriorType
an enumeration to select the prior
@ DIRICHLET_FROM_BAYESNET
@ DIRICHLET_FROM_DATABASE
bool isEnabledMinEpsilonRate() const override
void erasePossibleEdge(const Edge &edge)
void setNumberOfThreads(Size nb) override
sets the number max of threads that can be used
void useScoreBIC()
indicate that we wish to use a BIC score
void allowArcTriangleDeletions(bool allow=true)
allow (true)/forbid (false) to delete arc triangles during learning.
const std::vector< double > & EMHistory() const
returns the history of the last EM execution
Size nbDecreasingChanges_
StructuralConstraintNoChildrenNodes constraintNoChildrenNodes_
the constraint on no children nodes
DAG initialDAG()
returns the initial DAG structure
void EMsetVerbosity(bool v)
sets or unsets EM's verbosity
void setPossibleEdges(const EdgeSet &set)
assign a set of possible edges
Size maxIter() const override
void useNoPrior()
use no prior
ScoreType scoreType_
the score selected for learning
bool EMVerbosity() const
returns the EM's verbosity status
const ApproximationScheme * currentAlgorithm_
void eraseForbiddenArc(const Arc &arc)
void useSmoothingPrior(double weight=1)
use the prior smoothing
bool isEnabledEpsilon() const override
PriorType getPriorType_() const
returns the type (as a string) of a given prior
void allowArcAdditions(bool allow=true)
allow (true)/forbid (false) to add arcs during learning.
double alphaFci_
FCI parameters.
void useLocalSearchWithTabuList(Size tabu_size=100, Size nb_decrease=2)
indicate that we wish to use a local search with tabu list
void useScoreK2()
indicate that we wish to use a K2 score
double alphaPc_
PC parameters.
StructuralConstraintIndegree constraintIndegree_
the constraint for indegrees
bool allowArcDeletions_
whether we allow or not arc deletions during learning
void _setPriorWeight_(double weight)
sets the prior weight
bool verbosity() const override
verbosity
void useGreedyThickThinning()
indicate that we wish to use greedy thick-thinning
void disableMaxTime() override
Disable stopping criterion on timeout.
double currentTime() const override
get the current running time in second (double)
void disableEpsilon() override
Disable stopping criterion on epsilon.
void disableMaxIter() override
Disable stopping criterion on max iterations.
void useG2Test()
indicate that we wish to use G2 independence test for PC
void setPossibleSkeleton(const UndiGraph &skeleton)
assign a set of possible edges
bool exhaustiveSepSetFci_
void useEMWithRateCriterion(const double epsilon, const double noise=default_EM_noise)
use The EM algorithm to learn parameters with the rate stopping criterion
void useNMLCorrection()
indicate that we wish to use the NML correction for and MIIC
void useEM(const double epsilon, const double noise=default_EM_noise)
use The EM algorithm to learn parameters
void useEMWithDiffCriterion(const double epsilon, const double noise=default_EM_noise)
use The EM algorithm to learn parameters with the diff stopping criterion
bool hasMissingValues() const
returns true if the learner's database has missing values
void forbidEM()
prevent using the EM algorithm for parameter learning
bool EMisEnabledMaxIter() const
NodeId idFromName(std::string_view var_name) const
returns the node id corresponding to a variable name
Score * score_
the score used
void setPCMaxCondSetSize(Size max_k)
set maximum conditioning set size for PC (default Size(-1) = unlimited)
StructuralConstraintMandatoryArcs constraintMandatoryArcs_
the constraint on mandatory arcs
Miic algoMiic_
the Constraint MIIC algorithm
void unsetSliceOrder()
removes the slice order constraint
void EMenableMaxTime()
sets the stopping criterion of EM as being the minimal difference between two consecutive log-likelih...
EMApproximationScheme & EM()
returns the EM parameter learning approximation scheme if EM is enabled
IndepTestType indepTestTypePC_
void useNoCorrection()
indicate that we wish to use the NoCorr correction for MIIC
StructuralConstraintForbiddenArcs constraintForbiddenArcs_
the constraint on forbidden arcs
StructuralConstraintTotalOrder constraintTotalOrder_
the total order ing constraint
void useScoreLog2Likelihood()
indicate that we wish to use a Log2Likelihood score
void setRecordWeight(const std::size_t i, const double weight)
sets the weight of the ith record of the database
void useDirichletPrior(std::string_view filename, double weight=1)
use the Dirichlet prior from a database
void unsetTotalOrder()
removes the current total ordering constraint, if any
GreedyHillClimbing greedyHillClimbing_
the greedy hill climbing algorithm
void useMDLCorrection()
indicate that we wish to use the MDL correction for MIIC
void setFCIAlpha(double alpha)
set the significance threshold alpha for FCI (default 0.05)
bool fciExhaustiveSepSet() const
return true when FCI uses exhaustive sepset mode
void setPCAlpha(double alpha)
set the significance threshold alpha for PC (default 0.05)
void setVerbosity(bool v) override
verbosity
StructuralConstraintTabuList constraintTabuList_
the constraint for tabu lists
void addForbiddenArc(const Arc &arc)
DAG initialDag_
an initial DAG given to learners
void addNoChildrenNode(NodeId node)
GreedyThickThinning greedyThickThinning_
the greedy thick-thinning algorithm
void EMsetMaxTime(double timeout)
add a stopping criterion on timeout
ApproximationSchemeSTATE stateApproximationScheme() const override
history
void EMenableMinEpsilonRate()
Enable the log-likelihood evolution rate stopping criterion.
void useScoreMDL()
indicate that we wish to use a MDL score
void setFCIExhaustiveSepSet(bool exhaustive)
enable exhaustive sepset mode for FCI skeleton learning (default false)
Size domainSize(NodeId var) const
learn a structure from a file (must have read the db before)
void useScorefNML()
indicate that we wish to use a fNML score
void setTotalOrder(const Sequence< NodeId > &order)
sets a total order over some nodes
void useScoreAIC()
indicate that we wish to use an AIC score
bool allowArcReversals_
whether we allow or not arc reversals during learning
const std::vector< std::string > & names() const
returns the names of the variables in the database
Size EMPeriodSize() const
sets the stopping criterion of EM as being the minimal difference between two consecutive log-likelih...
void eraseMandatoryArc(const Arc &arc)
double EMCurrentTime() const
get the current running time in second (double)
void allowArcReversals(bool allow=true)
allow (true)/forbid (false) to reverse arcs during learning.
void useMIIC()
indicate that we wish to use MIIC
LocalSearchWithTabuList localSearchWithTabuList_
the local search with tabu list algorithm
void setCurrentApproximationScheme(const ApproximationScheme *approximationScheme)
{@ /// distribute signals
StructuralConstraintSliceOrder constraintSliceOrder_
the constraint for 2TBNs
const DatabaseTable & database() const
returns the database used by the BNLearner
bool EMisEnabledMinEpsilonRate() const
void EMdisableMaxTime()
Disable EM's timeout stopping criterion.
void eraseNoParentNode(NodeId node)
void setPCUnshieldedColliderSorted(bool sorted)
set unshielded-collider ordering for PC: sorted=true uses descending p-value order (strongest evidenc...
void EMsetEpsilon(double eps)
sets the stopping criterion of EM as being the minimal difference between two consecutive log-likelih...
void enableMaxIter() override
Enable stopping criterion on max iterations.
void setPCStable(bool stable)
set stable mode for PC — defer removals to end of each depth level (default true)
CorrectedMutualInformation::KModeTypes kmodeMiic_
the penalty used in MIIC
double minEpsilonRate() const override
Get the value of the minimal epsilon rate.
void useScoreBD()
indicate that we wish to use a BD score
bool isConstraintBased() const
indicate if the selected algorithm is constraint-based
std::string EMStateMessage() const
returns the state of the EM algorithm
the structural constraint imposing a partial order over nodes
the structural constraint imposing a total order over some nodes
#define GUM_ERROR(type, msg)
std::size_t Size
In aGrUM, hashed values are unsigned long int.
Set< Edge > EdgeSet
Some typdefs and define for shortcuts ...
Size NodeId
Type for node ids.
Set< Arc > ArcSet
Some typdefs and define for shortcuts ...
HashTable< NodeId, VAL > NodeProperty
Property on graph elements.
include the inlined functions if necessary
#define GUM_EMIT1(signal, arg1)
#define GUM_EMIT3(signal, arg1, arg2, arg3)
Base classes for undirected graphs.